Locus 10317

Sequence ID	3R_DroMel_CAF1
Location	27,696,240 – 27,696,378
Length	138
Max. P	0.906117

overview

Window 3

Location	27,696,240 – 27,696,344
Length	104
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	78.44
Mean single sequence MFE	-22.60
Consensus MFE	-13.42
Energy contribution	-14.62
Covariance contribution	1.20
Combinations/Pair	1.10
Mean z-score	-1.93
Structure conservation index	0.59
SVM decision value	0.62
SVM RNA-class probability	0.802185
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27696240 104 + 27905053
CACCAAACACAUGCAAACACAUGCAAACAACAAGCGCUUAGA-AAGCAAGCAUUUGCAUGAGCACUGAGAAAAAGGGGAUCUUGA---CU-AAAUGGAGACAUCCAUAU
..((.......((((......)))).......((.(((((..-..((((....)))).))))).))........))((((.((..---(.-....)..)).)))).... ( -19.40)
>DroSec_CAF1 18733 100 + 1
CGCCCGA---GUGCAAACACAUGCAAACAACAAGCGCUUGGA-AAGCAAGCAUUUGCAUGAGCACUGAGAAAAAGUGGAUCUUGAAAACUGAAAGGGAGA--UUAA---
..(((.(---((.(((...(((((((((.....).(((((..-...))))).))))))))..((((.......))))....)))...)))....)))...--....--- ( -23.30)
>DroSim_CAF1 18837 100 + 1
CGCCCGA---GUGCAAACACAUGCAAACAACAAGCGCUUGGA-AAGCAAGCAUUUGCAUGAGCACUGAGAAAAAGUGGAUCUUGAAAACUGAAAGGGAGA--UUAA---
..(((.(---((.(((...(((((((((.....).(((((..-...))))).))))))))..((((.......))))....)))...)))....)))...--....--- ( -23.30)
>DroEre_CAF1 18956 88 + 1
----------------ACACACACAAACAACCAGCGCUUGAAAAAGCGAGCGUUUGCAUGAGCACUGAGAGAAAGUGCAUCUCGAAAAGUAAAAGGGACU--CUAA---
----------------...((..(((((......(((((....)))))...)))))..)).(((((.......))))).((((...........))))..--....--- ( -20.60)
>DroYak_CAF1 19243 101 + 1
CAGCCCA---GUGCACACACAUGCAAACAACAAGCGCUUGGAAAAGCAAGCAUUUGCAUGAGCACUGAGAAAAAGUGCAUCUCGAAACCCAAAUGGGAGA--CUAU---
...((((---.........(((((((((.....).(((((......))))).)))))))).(((((.......)))))...............))))...--....--- ( -26.40)
>consensus
CACCCGA___GUGCAAACACAUGCAAACAACAAGCGCUUGGA_AAGCAAGCAUUUGCAUGAGCACUGAGAAAAAGUGGAUCUUGAAAACUAAAAGGGAGA__UUAA___
..(((..............(((((((((.....).(((((......))))).))))))))..((((.......)))).................)))............ (-13.42 = -14.62 +   1.20)

alignment

secondary structure

dotplot

Window 4

Location	27,696,240 – 27,696,344
Length	104
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	78.44
Mean single sequence MFE	-24.30
Consensus MFE	-15.38
Energy contribution	-14.74
Covariance contribution	-0.64
Combinations/Pair	1.22
Mean z-score	-1.61
Structure conservation index	0.63
SVM decision value	0.06
SVM RNA-class probability	0.562534
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27696240 104 - 27905053
AUAUGGAUGUCUCCAUUU-AG---UCAAGAUCCCCUUUUUCUCAGUGCUCAUGCAAAUGCUUGCUU-UCUAAGCGCUUGUUGUUUGCAUGUGUUUGCAUGUGUUUGGUG
..(((((....)))))..-..---.................((((.((.(((((((((((.(((..-....(((....)))....))).))))))))))).)))))).. ( -24.10)
>DroSec_CAF1 18733 100 - 1
---UUAA--UCUCCCUUUCAGUUUUCAAGAUCCACUUUUUCUCAGUGCUCAUGCAAAUGCUUGCUU-UCCAAGCGCUUGUUGUUUGCAUGUGUUUGCAC---UCGGGCG
---....--...(((............(((.........))).(((((.((((((((((((((...-..))))).......))))))))).....))))---).))).. ( -22.71)
>DroSim_CAF1 18837 100 - 1
---UUAA--UCUCCCUUUCAGUUUUCAAGAUCCACUUUUUCUCAGUGCUCAUGCAAAUGCUUGCUU-UCCAAGCGCUUGUUGUUUGCAUGUGUUUGCAC---UCGGGCG
---....--...(((............(((.........))).(((((.((((((((((((((...-..))))).......))))))))).....))))---).))).. ( -22.71)
>DroEre_CAF1 18956 88 - 1
---UUAG--AGUCCCUUUUACUUUUCGAGAUGCACUUUCUCUCAGUGCUCAUGCAAACGCUCGCUUUUUCAAGCGCUGGUUGUUUGUGUGUGU----------------
---..((--(((.......)))))..((((.......)))).....((.(((((((((((((((((....)))))..)).)))))))))).))---------------- ( -20.20)
>DroYak_CAF1 19243 101 - 1
---AUAG--UCUCCCAUUUGGGUUUCGAGAUGCACUUUUUCUCAGUGCUCAUGCAAAUGCUUGCUUUUCCAAGCGCUUGUUGUUUGCAUGUGUGUGCAC---UGGGCUG
---.(((--((((((....)))....((((.........))))(((((.((((((...(((((......)))))((.........)).)))))).))))---))))))) ( -31.80)
>consensus
___UUAA__UCUCCCUUUCAGUUUUCAAGAUCCACUUUUUCUCAGUGCUCAUGCAAAUGCUUGCUU_UCCAAGCGCUUGUUGUUUGCAUGUGUUUGCAC___UCGGGCG
..............................................((.(((((((((((.(((((....)))))...).)))))))))).))................ (-15.38 = -14.74 +  -0.64)

alignment

secondary structure

dotplot

Window 5

Location	27,696,274 – 27,696,378
Length	104
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	73.55
Mean single sequence MFE	-25.68
Consensus MFE	-8.92
Energy contribution	-8.96
Covariance contribution	0.04
Combinations/Pair	1.20
Mean z-score	-2.01
Structure conservation index	0.35
SVM decision value	1.05
SVM RNA-class probability	0.906117
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27696274 104 + 27905053
CGCUUAGA-AAGCAAGCAUUUGCAUGAGCACUGAGAAAAAGGGGAUCUUGA---CU-AAAUGGAGACAUCCAUAUAUGUAAAUGUCUAAAUACGGCAAAGAUUUUAUCA------
.(((((..-..((((....)))).)))))............((((((((.(---((-(.(((((....))))).)).))...((((.......))))))))))))....------ ( -20.10)
>DroSec_CAF1 18764 98 + 1
CGCUUGGA-AAGCAAGCAUUUGCAUGAGCACUGAGAAAAAGUGGAUCUUGAAAACUGAAAGGGAGA--UUAA----------UG----CAUCCAGCCCUAGUUUUAUAAGAAGCU
.(((((..-...)))))....((.....((((.......))))..(((((((((((...((((.((--(...----------..----.)))...)))))))))).))))).)). ( -24.20)
>DroSim_CAF1 18868 98 + 1
CGCUUGGA-AAGCAAGCAUUUGCAUGAGCACUGAGAAAAAGUGGAUCUUGAAAACUGAAAGGGAGA--UUAA----------UG----CAUCCAGCCCUAGUUUUAUAAGAAGCU
.(((((..-...)))))....((.....((((.......))))..(((((((((((...((((.((--(...----------..----.)))...)))))))))).))))).)). ( -24.20)
>DroEre_CAF1 18974 99 + 1
CGCUUGAAAAAGCGAGCGUUUGCAUGAGCACUGAGAGAAAGUGCAUCUCGAAAAGUAAAAGGGACU--CUAA----------UG----CAUAGGGUCCCACUUUUAUUUGAAGCC
(((((....))))).((.((((...(((((((.......))))).)).))))((((((((((((((--(((.----------..----..)))))))))..))))))))...)). ( -34.00)
>DroYak_CAF1 19274 99 + 1
CGCUUGGAAAAGCAAGCAUUUGCAUGAGCACUGAGAAAAAGUGCAUCUCGAAACCCAAAUGGGAGA--CUAU----------UG----UGUUCAGUCCUACUUUAAUUAGAAGCA
.(((((((...((((....)))).((((((((((((.........))))).......(((((....--))))----------))----)))))).)))..((......)))))). ( -25.90)
>consensus
CGCUUGGA_AAGCAAGCAUUUGCAUGAGCACUGAGAAAAAGUGGAUCUUGAAAACUAAAAGGGAGA__UUAA__________UG____CAUACAGCCCUACUUUUAUAAGAAGCU
.(((((......)))))....((.....((((.......))))..((((...........))))..............................))................... ( -8.92 =  -8.96 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:53:57 2006